Genomic epidemiology and evolution of duck hepatitis a virus

Abstract

Duck hepatitis A virus (DHAV), an avian picornavirus, causes high‐mortality acute disease in ducklings. Among the three serotypes, DHAV‐1 is globally distributed, whereas DHAV‐2 and DHAV‐3 serotypes are chiefly restricted to Southeast Asia. In this study, we analyzed the genomic evolution of DHAV‐1 strains using extant GenBank records and genomic sequences of 10 DHAV‐1 strains originating from a large disease outbreak in 2004–2005, in Hungary. Recombination analysis revealed intragenotype recombination within DHAV‐1 as well as intergenotype recombination events involving DHAV‐1 and DHAV‐3 strains. The intergenotype recombination occurred in the VP0 region. Diversifying selection seems to act at sites of certain genomic regions. Calculations estimated slightly lower rates of evolution of DHAV‐1 (mean rates for individual protein coding regions, 5.6286 × 10−4 to 1.1147 × 10−3 substitutions per site per year) compared to other picornaviruses. The observed evolutionary mechanisms indicate that whole‐genome‐based analysis of DHAV strains is needed to better understand the emergence of novel strains and their geographical dispersal.